Right, this wasn’t an obvious one. Basically you must run some audio through an effect, or some MIDI through a synth before the plugin will register parameter changes. So when I simply dropped an AU plugin onto a track, made some changes and saved, Logic wasn’t registering any of the changes. As soon as I hit play it then records the state of the parameters.
I’d be lying if I said this is the first time I got stung by this, but alas it’s not I guess in 99% of cases you will probably run some audio through a plugin before making any saves, so I think we’re good here?